Adding video to a logo

I don't know why I didn't think of this sooner, but another option is to cut your videos together and add your dissolves. Then place a black color matte underneath that video layer. Nest those two layers together. Put you logo above your nested layer. Then do the Track Matte Key.

Not sure exactly your setup and everything, and I know I've done this in the past before but couldn't remember exactly. So I started playing around. And the quickest thing I could think of off the top of my head was to place a copy of the logo under your you're video and logo tracks with the track matte. So my video layers were V4 - black png logo. V3 - footage with Track Matte effect. V2 - second black logo png. V1 - regular video layer or what ever. This way when the video with the Track Matte fades out it revearls just the black logo. If that makes sense. Perhaps someone else has a better way?

You might want to try moving the two video layers that you have track matted up and place the logo beneath them in the timeline. So when the track matte fades out you see the logo?